I've never used the server.app, but I assume it is launched by launchd from /System/Library/LaunchAgents or /System/Library/LaunchDaemons. Find the .plist file, then do this in a Terminal window:
launchctl unload -w /System/Library/LaunchDaemons/com.apple.whatever
Put the Server app in the trash and wait for the notification that it was removed and that services were stopped. You may need to empty the trash to install your app. If so, do that and then reinstall the Server after your other install.